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DHPS_ECOLI_1_282

Dihydropteroate synthase [DHPS family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DHPS_ECOLI):D: Pterin-binding (20, 22, 56, 59, 61:64, 96, 115, 117, 137, 139, 185, 189, 190, 215, 217, 219:222, 232, 235, 255, 257)
R: 6-hydroxymethyl-7,8-dihydropterin diphosphate binding (255, 257)
20, 22, 56, 59, 61:64, 96, 115, 117, 137, 139, 185, 189, 190, 215, 217, 219:222, 232, 235, 255, 257

Full PDB list

1aj0, 1aj2, 1ajz, 5u0v, 5u0w, 5u0y, 5u0z, 5u10, 5u11, 5u12, 5u13, 5u14, 5v79, 5v7a

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
0
N
2
2
T
6
2
R
6
3
P
6
4
D
9
6
N
1
1
5
I
1
1
7
C
1
3
7
M
1
3
9
D
1
8
5
G
1
8
9
F
1
9
0
L
2
1
5
G
2
1
7
S
2
1
9
R
2
2
0
K
2
2
1
S
2
2
2
R
2
5
5
H
2
5
7
[1]1aj0.a ph2,san25 . . . . . . . . . . . . . . . . . . . . .
[1]1aj2.a 2ph22 . . . . . . . . . . . . . . . . . . . . .
[1]1ajz.a none . . . . . . . . . . . . . . . . . . . . .
[1]5u0v.a 7vj12 . . . . . . . . . . . . . . . . . . . . .
[1]5u0w.a 9mg12 . . . . . . . . . . . . . . . . . . . . .
[1]5u0y.a 7pj16 . . . . . . . . . . . . . . . . . . . . .
[1]5u0z.b 7pm22 . . . . . . . . . . . . . . . . . . . . .
[1]5u10.a pt123 . . . . . . . . . . . . . . . . . . . . .
[1]5u11.a 7ps17 . . . . . . . . . . . . . . . . . . . . .
[1]5u12.a 5ru20 . . . . . . . . . . . . . . . . . . . . .
[1]5u13.a yh523 . . . . . . . . . . . . . . . . . . . . .
[1]5u14.a 7pv24 . . . . . . . . . . . . . . . . . . . . .
[1]5v79.a 8y423 . . . . . . . . . . . . . . . . . . . . .
[1]5v7a.b 8y717 . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
I
2
0
N
2
2
D
5
6
G
5
9
S
6
1
T
6
2
R
6
3
P
6
4
D
9
6
N
1
1
5
I
1
1
7
C
1
3
7
M
1
3
9
D
1
8
5
G
1
8
9
F
1
9
0
L
2
1
5
G
2
1
7
S
2
1
9
R
2
2
0
K
2
2
1
S
2
2
2
P
2
3
2
R
2
3
5
R
2
5
5
H
2
5
7
[1]1aj0.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]1aj2.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]1ajz.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]5u0v.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u0w.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u0y.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u0z.b . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u10.a . . . . . . * . * . . . . . . . . . . . . . . . . .
[1]5u11.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]5u12.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u13.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u14.a . . . . . . * . * . . . . . . . . . . . . . . . . .
[1]5v79.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5v7a.b . . . . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1aj0.a:ph2,san
1aj2.a:2ph
1ajz.a is apo
5u0v.a:7vj
5u0w.a:9mg
5u0y.a:7pj
5u0z.b:7pm
5u10.a:pt1
5u11.a:7ps
5u12.a:5ru
5u13.a:yh5
5u14.a:7pv
5v79.a:8y4
5v7a.b:8y7
[1] 1aj0.a
0.2
0 - 0.4 0.3 0.1 1.2 0 0.1 0.2 0 0.2 0.2 0.1
[1] 1aj2.a 0.2
0
- 0.4 0.3 0 1.1 0 0 0.1 0 0.3 0.4 0.4
[1] 1ajz.a 0.4 0.3
-
0.2 0.2 0.5 1.7 0.5 0.5 0.6 0.3 0.6 0.5 0.3
[1] 5u0v.a 0.2 0.5 -
0.1
0.1 0.1 1.0 0 0.1 0.1 0.1 0.1 0.1 0.1
[1] 5u0w.a 0.2 0.2 - 0
0.1
0.3 0.7 0 0.3 0.1 0.2 0.3 0.2 0.2
[1] 5u0y.a 0.1 0.1 - 0.4 0.4
0.1
0 0 0.1 0.1 0.1 0.5 0.5 0.5
[1] 5u0z.b 0.1 0.5 - 0.1 0.1 0.1
0
0 0.2 0.1 0.1 0.2 0.1 0.1
[1] 5u10.a 0.2 0.2 - 1.0 0.5 0.2 1.9
0
0.2 0.1 0.1 0.2 0.6 0.6
[1] 5u11.a 0.2 0.1 - 0.5 0.4 0 1.2 0.1
0
0 0.1 0.1 0.4 0.5
[1] 5u12.a 0.1 0.3 - 0.2 0.1 0.2 1.2 0.1 0.2
0.2
0.2 0.4 0.2 0.2
[1] 5u13.a 0.1 0.2 - 0.7 0.5 0.3 0.8 0 0.2 0.3
0.1
0.3 0.4 0.4
[1] 5u14.a 0.1 0 - 0.9 0.4 0 1.4 0 0 0.1 0
0
0.4 0.4
[1] 5v79.a 0 0.1 - 0 0 0 0.2 0.2 0 0.1 0 0.4
0
0
[1] 5v7a.b 0 0.4 - 0 0 0 1.4 0 0 0 0 0.1 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1aj0.a
1aj2.a
1ajz.a
5u0v.a
5u0w.a
5u0y.a
5u0z.b
5u10.a
5u11.a
5u12.a
5u13.a
5u14.a
5v79.a
5v7a.b
[1] 1aj0.a
0
.01 .05 .08 .05 .07 .06 .05 .02 .05 .04 .04 .08 .05
[1] 1aj2.a .01
0
.05 .07 .04 .06 .06 .05 .02 .05 .03 .05 .08 .05
[1] 1ajz.a .05 .05
0
.08 .05 .07 .06 .09 .05 .04 .06 .08 .07 .05
[1] 5u0v.a .08 .07 .08
0
.04 .07 .03 .10 .07 .04 .06 .09 .06 .03
[1] 5u0w.a .05 .04 .05 .04
0
.06 .02 .09 .05 .04 .02 .08 .04 .04
[1] 5u0y.a .07 .06 .07 .07 .06
0
.05 .10 .07 .06 .05 .09 .02 .08
[1] 5u0z.b .06 .06 .06 .03 .02 .05
0
.09 .06 .04 .04 .08 .04 .04
[1] 5u10.a .05 .05 .09 .10 .09 .10 .09
0
.05 .08 .07 .02 .12 .08
[1] 5u11.a .02 .02 .05 .07 .05 .07 .06 .05
0
.05 .03 .03 .07 .04
[1] 5u12.a .05 .05 .04 .04 .04 .06 .04 .08 .05
0
.05 .07 .05 .03
[1] 5u13.a .04 .03 .06 .06 .02 .05 .04 .07 .03 .05
0
.07 .06 .07
[1] 5u14.a .04 .05 .08 .09 .08 .09 .08 .02 .03 .07 .07
0
.11 .06
[1] 5v79.a .08 .08 .07 .06 .04 .02 .04 .12 .07 .05 .06 .11
0
.07
[1] 5v7a.b .05 .05 .05 .03 .04 .08 .04 .08 .04 .03 .07 .06 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1aj0.a
1aj2.a
1ajz.a
5u0v.a
5u0w.a
5u0y.a
5u0z.b
5u10.a
5u11.a
5u12.a
5u13.a
5u14.a
5v79.a
5v7a.b
[1] 1aj0.a
0
0.3 0.3 1.2 0.6 0.9 2.4 0.6 0.5 0.8 0.6 0.6 0.8 1.0
[1] 1aj2.a 0.3
0
0.4 1.3 0.7 0.9 2.5 0.7 0.7 1.0 0.7 0.7 0.7 1.1
[1] 1ajz.a 0.3 0.4
0
1.2 0.6 0.9 2.3 0.7 0.6 0.8 0.6 0.7 0.8 1.0
[1] 5u0v.a 1.2 1.3 1.2
0
1.1 1.5 1.7 1.1 1.2 1.1 1.1 1.1 1.4 0.9
[1] 5u0w.a 0.6 0.7 0.6 1.1
0
0.8 2.4 0.3 0.2 0.6 0.2 0.3 0.8 1.0
[1] 5u0y.a 0.9 0.9 0.9 1.5 0.8
0
2.5 1.0 0.8 0.9 0.8 0.9 0.4 1.3
[1] 5u0z.b 2.4 2.5 2.3 1.7 2.4 2.5
0
2.4 2.4 2.1 2.4 2.4 2.5 1.9
[1] 5u10.a 0.6 0.7 0.7 1.1 0.3 1.0 2.4
0
0.3 0.7 0.2 0.2 0.9 1.0
[1] 5u11.a 0.5 0.7 0.6 1.2 0.2 0.8 2.4 0.3
0
0.7 0.2 0.2 0.7 1.0
[1] 5u12.a 0.8 1.0 0.8 1.1 0.6 0.9 2.1 0.7 0.7
0
0.7 0.7 0.9 0.8
[1] 5u13.a 0.6 0.7 0.6 1.1 0.2 0.8 2.4 0.2 0.2 0.7
0
0.2 0.7 1.0
[1] 5u14.a 0.6 0.7 0.7 1.1 0.3 0.9 2.4 0.2 0.2 0.7 0.2
0
0.8 1.0
[1] 5v79.a 0.8 0.7 0.8 1.4 0.8 0.4 2.5 0.9 0.7 0.9 0.7 0.8
0
1.2
[1] 5v7a.b 1.0 1.1 1.0 0.9 1.0 1.3 1.9 1.0 1.0 0.8 1.0 1.0 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1aj0.a
1aj2.a
1ajz.a
5u0v.a
5u0w.a
5u0y.a
5u0z.b
5u10.a
5u11.a
5u12.a
5u13.a
5u14.a
5v79.a
5v7a.b
[1] 1aj0.a
0
0.6 0.6 1.6 1.1 1.2 2.5 0.8 0.7 0.8 1.0 0.8 1.5 1.1
[1] 1aj2.a 0.6
0
0.7 1.7 1.1 1.2 2.6 0.8 0.8 1.0 1.1 0.9 1.4 1.3
[1] 1ajz.a 0.6 0.7
0
1.7 1.2 1.3 2.5 1.0 0.9 0.9 1.2 1.0 1.6 1.2
[1] 5u0v.a 1.6 1.7 1.7
0
1.2 1.6 1.6 1.5 1.4 1.4 1.3 1.4 1.6 1.2
[1] 5u0w.a 1.1 1.1 1.2 1.2
0
0.9 2.3 0.8 0.8 1.0 0.4 0.8 1.1 1.2
[1] 5u0y.a 1.2 1.2 1.3 1.6 0.9
0
2.4 1.2 1.1 1.2 0.9 1.1 0.9 1.4
[1] 5u0z.b 2.5 2.6 2.5 1.6 2.3 2.4
0
2.5 2.4 2.1 2.3 2.4 2.5 1.9
[1] 5u10.a 0.8 0.8 1.0 1.5 0.8 1.2 2.5
0
0.6 0.9 0.8 0.8 1.4 1.1
[1] 5u11.a 0.7 0.8 0.9 1.4 0.8 1.1 2.4 0.6
0
0.8 0.7 0.7 1.3 1.1
[1] 5u12.a 0.8 1.0 0.9 1.4 1.0 1.2 2.1 0.9 0.8
0
1.0 0.9 1.5 0.8
[1] 5u13.a 1.0 1.1 1.2 1.3 0.4 0.9 2.3 0.8 0.7 1.0
0
0.8 1.1 1.2
[1] 5u14.a 0.8 0.9 1.0 1.4 0.8 1.1 2.4 0.8 0.7 0.9 0.8
0
1.4 1.2
[1] 5v79.a 1.5 1.4 1.6 1.6 1.1 0.9 2.5 1.4 1.3 1.5 1.1 1.4
0
1.6
[1] 5v7a.b 1.1 1.3 1.2 1.2 1.2 1.4 1.9 1.1 1.1 0.8 1.2 1.2 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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